Busco issue

[qfaber]

Hi, I am unable to install the recommended version of Busco via conda and the code is no longer available else so I have a newer version: 5.4.3. I ran EUKulele and I don't think busco worked with the latest version- is there a way I can fix this? Thanks!

[akrinos]

Hi @qfaber , we are so excited that you are using EUKulele! So sorry for the trouble with BUSCO. First question: is it important to you to have the BUSCO steps done? If not, I've added a flag to ignore those steps, because of how often that particular piece of the pipeline was problematic. If so, we can talk other potential solutions!

[qfaber]

Yes, it is. It seems to be running fine now- I'm getting output folders for taxonomy, but not folders for core_taxonomy or busco_assessment

[akrinos]

Hello @qfaber - EUKulele has completed without the BUSCO steps, you mean? If you could send the output messages it got to, that would help with diagnosing. Thanks!

[qfaber]

Yes, that's what I mean. I attached the output- it ran for several hours on the final step without doing anything, maybe that was the issue. I can also send error logs if that is helpful. Thanks!

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From: akrinos @.> Sent: Tuesday, January 17, 2023 5:46 PM To: AlexanderLabWHOI/EUKulele @.> Cc: Faber,Quincy L @.>; Mention @.> Subject: Re: [AlexanderLabWHOI/EUKulele] Busco issue (Issue #49)

[External Email]

Hello @qfaberhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fqfaber&data=05%7C01%7Cqfaber%40ufl.edu%7C5acc81b1f5dc4201520b08daf8dca6ea%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638095923824356168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dESPYwc%2BX%2FEpPeKdq4x0ts6ZngiGNmNSjEGgT1Q5hgc%3D&reserved=0 - EUKulele has completed without the BUSCO steps, you mean? If you could send the output messages it got to, that would help with diagnosing. Thanks!

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EUKulele --sample_dir /media/racheljoyce/HDD2/meta_euk/euk_bins -m mags

Running EUKulele with command line arguments, as no valid configuration file was provided. Setting things up... Specified reference directory, reference FASTA, and protein map/taxonomy table not found. Using database in location: ./marmmetsp. Found database folder for ./marmmetsp in current directory; will not re-download. Creating a diamond reference from database files... Diamond database file already created; will not re-create database. Aligning to reference database... Aligning sample all_2014.5.fa... Aligning sample near-ice_2015.4.fa... Aligning sample near-ice_2015.8.fa... Aligning sample englacial_2015.2.fa... Aligning sample near-ice_2015.10.fa... Aligning sample all_2014.1.fa... Aligning sample all_2014.7.fa... Aligning sample wca_2015.2.fa... Aligning sample near-ice_2015.1.fa... Aligning sample englacial_2015.1.fa... Aligning sample near-ice_2015.7.fa... Aligning sample near-ice_2015.6.fa... Diamond process exited for sample near-ice_2015.1.fa. Diamond process exited for sample all_2014.1.fa. Aligning sample near-ice_2015.9.fa... Aligning sample wca_2014.6.fa... Diamond process exited for sample englacial_2015.2.fa. Aligning sample wca_2014.3.fa... Diamond process exited for sample near-ice_2015.8.fa. Aligning sample all_2014.4.fa... Diamond process exited for sample englacial_2015.1.fa. Aligning sample wca_2014.2.fa... Diamond process exited for sample near-ice_2015.7.fa. Aligning sample near-ice_2015.12.fa... Diamond process exited for sample all_2014.7.fa. Aligning sample wca_2014.4.fa... Diamond process exited for sample near-ice_2015.4.fa. Aligning sample wca_2015.1.fa... Diamond process exited for sample all_2014.5.fa. Aligning sample near-ice_2015.14.fa... Diamond process exited for sample near-ice_2015.10.fa. Aligning sample near-ice_2015.13.fa... Diamond process exited for sample near-ice_2015.6.fa. Aligning sample near-ice_2015.3.fa... Diamond process exited for sample wca_2015.2.fa. Aligning sample near-ice_2015.2.fa... Diamond process exited for sample near-ice_2015.9.fa. Aligning sample wca_2014.5.fa... Diamond process exited for sample wca_2015.1.fa. Aligning sample near-ice_2015.11.fa... Diamond process exited for sample near-ice_2015.12.fa. Aligning sample near-ice_2015.15.fa... Diamond process exited for sample near-ice_2015.13.fa. Aligning sample all_2014.6.fa... Diamond process exited for sample near-ice_2015.3.fa. Aligning sample all_2014.3.fa... Diamond process exited for sample wca_2014.3.fa. Aligning sample englacial_2015.3.fa... Diamond process exited for sample near-ice_2015.14.fa. Aligning sample wca_2014.1.fa... Diamond process exited for sample wca_2014.2.fa. Aligning sample near-ice_2014.1.fa... Diamond process exited for sample wca_2014.6.fa. Aligning sample near-ice_2015.5.fa... Diamond process exited for sample near-ice_2015.2.fa. Aligning sample all_2014.2.fa... Diamond process exited for sample wca_2014.4.fa. Diamond process exited for sample all_2014.4.fa. Diamond process exited for sample wca_2014.5.fa. Diamond process exited for sample near-ice_2015.11.fa. Diamond process exited for sample all_2014.6.fa. Diamond process exited for sample englacial_2015.3.fa. Diamond process exited for sample wca_2014.1.fa. Diamond process exited for sample near-ice_2015.15.fa. Diamond process exited for sample all_2014.2.fa. Diamond process exited for sample all_2014.3.fa. Diamond process exited for sample near-ice_2014.1.fa. Diamond process exited for sample near-ice_2015.5.fa. Performing taxonomic estimation steps... Performing taxonomic visualization steps...

[akrinos]

The taxonomy estimation steps completed successfully with the dialog you attached?

[qfaber]

Yes, for each sample i got files labelled samplename-estimated-taxonomy.out

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From: akrinos @.> Sent: Tuesday, January 17, 2023 7:27 PM To: AlexanderLabWHOI/EUKulele @.> Cc: Faber,Quincy L @.>; Mention @.> Subject: Re: [AlexanderLabWHOI/EUKulele] Busco issue (Issue #49)

[External Email]

The taxonomy estimation steps completed successfully with the dialog you attached?

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[akrinos]

@qfaber sorry for not following up on this. Could you send error logs if you're still having these issues with it? thanks!

[akrinos]

Hi @qfaber - let me know if you still need help with EUKulele? Else I'll close up this issue. Thanks!